After graduating with his masters, he spent one year as an assistant at the University of New Hampshire under coach Bob Kullen, but Kullen fell ill and that left his job in jeopardy. Seeking stability, he accepted a position as an assistant coach at his alma mater in 1988, a position he held through the 1998–99 school year.

In his first six years at RIT, he compiled a 116–31–12 record (.767 winning percentage), with four ECAC West regular-season championships, three ECAC West tournament titles, and three NCAA tournament appearances. However, those all came in his first years at RIT; in 2003, the Tigers missed the D-III national tournament for the first time since 1995, and they would never return.

In late 2004, despite a couple of "down" years for the program (including "only" a 13–7–5 record in 2003–04), RIT President Albert J. Simone announced that RIT would move their hockey program up to the Division I level, retaining Wilson as head coach. RIT would join Atlantic Hockey starting in the 2006–07 season.

The rest of the 2004–05 campaign was rough, and the Tigers finished with their worst record of Wilson's tenure to date, including a painful loss to arch-rival Elmira College in which the Tigers squandered a late two-goal lead by allowing a pair of short-handed goals in the last three minutes of regulation.

The Tigers' first season as a Division I program, in which they played as an independent was even harder, although the highlight was a home win over the St. Lawrence Saints (ranked #18 in the nation at the time). The Tigers won only nine games that season, mostly against future Atlantic Hockey conference opponents.

In 2010, in recognition of reaching the Frozen Four, Wilson won the Spencer Penrose Award, for the top coach in Division I men's ice hockey. He became the first coach to win both the Spencer Penrose Award and the Edward Jeremiah Award. He also signed a five-year contract that year, keeping him at RIT until at least the 2014-15 season.

Wilson and his wife Lynn live in Pittsford, New York. Their daughter Stephanie attends Bowling Green State University, and their son Stuart is playing junior hockey.